Merge pull request #2466 from paulromano/nea-workshop-updates

Miscellaneous updates and improvements from NEA course

CMakeLists.txt

@@ -292,7 +292,7 @@ endif()
 
 if(OPENMC_BUILD_TESTS)
   find_package_write_status(Catch2)
-  if (NOT Catch2)
+  if (NOT Catch2_FOUND)
     add_subdirectory(vendor/Catch2)
   endif()
 endif()

README.md

@@ -15,7 +15,8 @@ project started under the Computational Reactor Physics Group at MIT.
 Complete documentation on the usage of OpenMC is hosted on Read the Docs (both
 for the [latest release](https://docs.openmc.org/en/stable/) and
 [developmental](https://docs.openmc.org/en/latest/) version). If you are
-interested in the project, or would like to help and contribute, please get in touch on the OpenMC [discussion forum](https://openmc.discourse.group/).
+interested in the project, or would like to help and contribute, please get in
+touch on the OpenMC [discussion forum](https://openmc.discourse.group/).
 
 ## Installation
 
@@ -36,20 +37,21 @@ citing the following publication:
 ## Troubleshooting
 
 If you run into problems compiling, installing, or running OpenMC, first check
-the [Troubleshooting section](https://docs.openmc.org/en/stable/usersguide/troubleshoot.html) in
-the User's Guide. If you are not able to find a solution to your problem there,
+the [Troubleshooting
+section](https://docs.openmc.org/en/stable/usersguide/troubleshoot.html) in the
+User's Guide. If you are not able to find a solution to your problem there,
 please post to the [discussion forum](https://openmc.discourse.group/).
 
 ## Reporting Bugs
 
 OpenMC is hosted on GitHub and all bugs are reported and tracked through the
-[Issues](https://github.com/openmc-dev/openmc/issues) feature on GitHub. However,
-GitHub Issues should not be used for common troubleshooting purposes. If you are
-having trouble installing the code or getting your model to run properly, you
-should first send a message to the User's Group mailing list. If it turns out
-your issue really is a bug in the code, an issue will then be created on
-GitHub. If you want to request that a feature be added to the code, you may
-create an Issue on github.
+[Issues](https://github.com/openmc-dev/openmc/issues) feature on GitHub.
+However, GitHub Issues should not be used for common troubleshooting purposes.
+If you are having trouble installing the code or getting your model to run
+properly, you should first send a message to the [discussion
+forum](https://openmc.discourse.group/). If it turns out your issue really is a
+bug in the code, an issue will then be created on GitHub. If you want to request
+that a feature be added to the code, you may create an Issue on github.
 
 ## License
 

docs/source/pythonapi/capi.rst

@@ -13,20 +13,28 @@ Functions
    :template: myfunction.rst
 
    calculate_volumes
+   current_batch
    export_properties
    finalize
    find_cell
    find_material
+   global_bounding_box
+   global_tallies
    hard_reset
+   id_map
    import_properties
    init
+   is_statepoint_batch
    iter_batches
    keff
    load_nuclide
+   master
    next_batch
    num_realizations
    plot_geometry
+   property_map
    reset
+   reset_timers
    run
    run_in_memory
    sample_external_source

openmc/data/library.py

@@ -5,24 +5,29 @@ import pathlib
 import h5py
 
 import openmc
-from openmc.mixin import EqualityMixin
 from openmc._xml import clean_indentation, reorder_attributes
 
 
-class DataLibrary(EqualityMixin):
+class DataLibrary(list):
     """Collection of cross section data libraries.
 
-    Attributes
-    ----------
-    libraries : list of dict
-        List in which each item is a dictionary summarizing cross section data
-        from a single file. The dictionary has keys 'path', 'type', and
-        'materials'.
+    This class behaves like a list where each item is a dictionary summarizing
+    cross section data from a single file. The dictionary has keys 'path',
+    'type', and 'materials'.
+
+    .. versionchanged:: 0.13.4
+        This class now behaves like a list rather than requiring you to access
+        the list of libraries through a special attribute.
 
     """
 
     def __init__(self):
-        self.libraries = []
+        super().__init__()
+
+    @property
+    def libraries(self):
+        # For backwards compatibility
+        return self
 
     def get_by_material(self, name, data_type='neutron'):
         """Return the library dictionary containing a given material.
@@ -43,11 +48,26 @@ class DataLibrary(EqualityMixin):
             the dictionary has keys 'path', 'type', and 'materials'.
 
         """
-        for library in self.libraries:
+        for library in self:
             if name in library['materials'] and data_type in library['type']:
                 return library
         return None
 
+    def remove_by_material(self, name: str, data_type='neutron'):
+        """Remove the library dictionary containing a specific material
+
+        Parameters
+        ----------
+        name : str
+            Name of material, e.g. 'Am241'
+        data_type : str
+            Name of data type, e.g. 'neutron', 'photon', 'wmp', or 'thermal'
+
+        """
+        library = self.get_by_material(name, data_type)
+        if library is not None:
+            self.remove(library)
+
     def register_file(self, filename):
         """Register a file with the data library.
 
@@ -77,7 +97,7 @@ class DataLibrary(EqualityMixin):
                 .format(path.name, self.__class__.__name__))
 
         library = {'path': str(path), 'type': filetype, 'materials': materials}
-        self.libraries.append(library)
+        self.append(library)
 
     def export_to_xml(self, path='cross_sections.xml'):
         """Export cross section data library to an XML file.
@@ -92,7 +112,7 @@ class DataLibrary(EqualityMixin):
 
         # Determine common directory for library paths
         common_dir = os.path.dirname(os.path.commonprefix(
-            [lib['path'] for lib in self.libraries]))
+            [lib['path'] for lib in self]))
         if common_dir == '':
             common_dir = '.'
 
@@ -100,7 +120,7 @@ class DataLibrary(EqualityMixin):
             dir_element = ET.SubElement(root, "directory")
             dir_element.text = os.path.realpath(common_dir)
 
-        for library in self.libraries:
+        for library in self:
             if library['type'] == "depletion_chain":
                 lib_element = ET.SubElement(root, "depletion_chain")
             else:

openmc/deplete/results.py

@@ -54,11 +54,11 @@ class Results(list):
 
     Parameters
     ----------
-    filename : str
+    filename : str, optional
         Path to depletion result file
 
     """
-    def __init__(self, filename=None):
+    def __init__(self, filename='depletion_results.h5'):
         data = []
         if filename is not None:
             with h5py.File(str(filename), "r") as fh:

openmc/filter.py

@@ -4,6 +4,7 @@ from collections.abc import Iterable
 import hashlib
 from itertools import product
 from numbers import Real, Integral
+import warnings
 from xml.etree import ElementTree as ET
 
 import numpy as np
@@ -588,7 +589,7 @@ class CellInstanceFilter(Filter):
     bins : iterable of 2-tuples or numpy.ndarray
         The cell instances to tally, given as 2-tuples. For the first value in
         the tuple, either openmc.Cell objects or their integral ID numbers can
-        be used.
+        be used. The second value indicates the cell instance.
     filter_id : int
         Unique identifier for the filter
 

openmc/mgxs/groups.py

@@ -5,30 +5,36 @@ from numbers import Real
 import numpy as np
 
 import openmc.checkvalue as cv
+import openmc.mgxs
 
 
 class EnergyGroups:
-    """An energy groups structure used for multi-group cross-sections.
+    """An energy group structure used for multigroup cross-sections.
 
     Parameters
     ----------
-    group_edges : Iterable of Real
-        The energy group boundaries [eV]
+    group_edges : Iterable of float or str
+        The energy group boundaries in [eV] or the name of the group structure
+        (Must be a valid key in the openmc.mgxs.GROUP_STRUCTURES dictionary).
+
+        .. versionchanged:: 0.13.4
+            Changed to allow a string specifying the group structure name.
 
     Attributes
     ----------
-    group_edges : Iterable of Real
-        The energy group boundaries [eV]
+    group_edges : np.ndarray
+        The energy group boundaries in [eV]
     num_groups : int
         The number of energy groups
 
     """
 
-    def __init__(self, group_edges=None):
-        self._group_edges = None
+    def __init__(self, group_edges):
+        if isinstance(group_edges, str):
+            self._name = group_edges.upper()
+            group_edges = openmc.mgxs.GROUP_STRUCTURES[self._name]
 
-        if group_edges is not None:
-            self.group_edges = group_edges
+        self.group_edges = group_edges
 
     def __deepcopy__(self, memo):
         existing = memo.get(id(self))
@@ -59,6 +65,12 @@ class EnergyGroups:
     def __hash__(self):
         return hash(tuple(self.group_edges))
 
+    def __repr__(self):
+        if hasattr(self, '_name'):
+            return f"<EnergyGroups: {self.num_groups} groups ({self._name})>"
+        else:
+            return f"<EnergyGroups: {self.num_groups} groups>"
+
     @property
     def group_edges(self):
         return self._group_edges
@@ -226,10 +238,7 @@ class EnergyGroups:
         group_edges = np.sort(group_edges)
 
         # Create a new condensed EnergyGroups object
-        condensed_groups = EnergyGroups()
-        condensed_groups.group_edges = group_edges
-
-        return condensed_groups
+        return EnergyGroups(group_edges)
 
     def can_merge(self, other):
         """Determine if energy groups can be merged with another.

openmc/model/triso.py

@@ -1206,7 +1206,7 @@ def _close_random_pack(domain, spheres, contraction_rate):
 
 
 def pack_spheres(radius, region, pf=None, num_spheres=None, initial_pf=0.3,
-                 contraction_rate=1.e-3, seed=1):
+                 contraction_rate=1.e-3, seed=None):
     """Generate a random, non-overlapping configuration of spheres within a
     container.
 
@@ -1235,7 +1235,7 @@ def pack_spheres(radius, region, pf=None, num_spheres=None, initial_pf=0.3,
         reached using a smaller contraction rate, but the algorithm will take
         longer to converge.
     seed : int, optional
-        RNG seed.
+        Pseudorandom number generator seed passed to :func:`random.seed`
 
     Returns
     ------
@@ -1278,7 +1278,8 @@ def pack_spheres(radius, region, pf=None, num_spheres=None, initial_pf=0.3,
 
     """
     # Seed RNG
-    random.seed(seed)
+    if seed is not None:
+        random.seed(seed)
 
     # Create container with the correct shape based on the supplied region
     domain = None
@@ -1310,14 +1311,13 @@ def pack_spheres(radius, region, pf=None, num_spheres=None, initial_pf=0.3,
 
     # Check packing fraction for close random packing
     if pf > MAX_PF_CRP:
-        raise ValueError('Packing fraction {0} is greater than the limit for '
-                         'close random packing, {1}'.format(pf, MAX_PF_CRP))
+        raise ValueError(f'Packing fraction {pf} is greater than the limit for '
+                         f'close random packing, {MAX_PF_CRP}')
 
     # Check packing fraction for random sequential packing
     if initial_pf > MAX_PF_RSP:
-        raise ValueError('Initial packing fraction {0} is greater than the '
-                         'limit for random sequential packing, '
-                         '{1}'.format(initial_pf, MAX_PF_RSP))
+        raise ValueError(f'Initial packing fraction {initial_pf} is greater than'
+                         f'the limit for random sequential packing, {MAX_PF_RSP}')
 
     # Calculate the sphere radius used in the initial random sequential
     # packing from the initial packing fraction

openmc/surface.py

@@ -737,16 +737,25 @@ class Plane(PlaneMixin, Surface):
         Plane
             Plane that passes through the three points
 
+        Raises
+        ------
+        ValueError
+            If all three points lie along a line
+
         """
         # Convert to numpy arrays
-        p1 = np.asarray(p1)
-        p2 = np.asarray(p2)
-        p3 = np.asarray(p3)
+        p1 = np.asarray(p1, dtype=float)
+        p2 = np.asarray(p2, dtype=float)
+        p3 = np.asarray(p3, dtype=float)
 
         # Find normal vector to plane by taking cross product of two vectors
         # connecting p1->p2 and p1->p3
         n = np.cross(p2 - p1, p3 - p1)
 
+        # Check for points along a line
+        if np.allclose(n, 0.):
+            raise ValueError("All three points appear to lie along a line.")
+
         # The equation of the plane will by n·(<x,y,z> - p1) = 0. Determine
         # coefficients a, b, c, and d based on that
         a, b, c = n

src/tallies/tally.cpp

@@ -191,9 +191,9 @@ Tally::Tally(pugi::xml_node node)
         case SCORE_DELAYED_NU_FISSION:
         case SCORE_PROMPT_NU_FISSION:
         case SCORE_DECAY_RATE:
-          warning("Particle filter is not used with photon transport"
-                  " on and " +
-                  reaction_name(score) + " score.");
+          warning("You are tallying the '" + reaction_name(score) +
+                  "' score and haven't used a particle filter. This score will "
+                  "include contributions from all particles.");
           break;
         }
       }
@@ -1283,7 +1283,8 @@ extern "C" int openmc_remove_tally(int32_t index)
   if (index < 0 || index > model::tallies.size()) {
     return OPENMC_E_OUT_OF_BOUNDS;
   }
-  // grab tally so it's ID can be obtained to remove the (ID,index) pair from tally_map
+  // grab tally so it's ID can be obtained to remove the (ID,index) pair from
+  // tally_map
   auto& tally = model::tallies[index];
   // delete the tally via iterator pointing to correct position
   // this calls the Tally destructor, removing the tally from the map as well

tests/regression_tests/triso/test.py

@@ -1,7 +1,3 @@
-import random
-from math import sqrt
-
-import numpy as np
 import openmc
 import openmc.model
 
@@ -65,8 +61,8 @@ class TRISOTestHarness(PyAPITestHarness):
         box = openmc.Cell(region=box_region)
 
         outer_radius = 422.5*1e-4
-        centers = openmc.model.pack_spheres(radius=outer_radius,
-            region=box_region, num_spheres=100)
+        centers = openmc.model.pack_spheres(
+            radius=outer_radius, region=box_region, num_spheres=100, seed=1)
         trisos = [openmc.model.TRISO(outer_radius, inner_univ, c)
             for c in centers]
 

tests/unit_tests/test_data_misc.py

@@ -11,7 +11,7 @@ import openmc.data
 
 def test_data_library(tmpdir):
     lib = openmc.data.DataLibrary.from_xml()
-    for f in lib.libraries:
+    for f in lib:
         assert sorted(f.keys()) == ['materials', 'path', 'type']
 
     f = lib.get_by_material('U235')
@@ -22,6 +22,9 @@ def test_data_library(tmpdir):
     assert f['type'] == 'thermal'
     assert 'c_H_in_H2O' in f['materials']
 
+    lib.remove_by_material('Pu239')
+    assert lib.get_by_material('Pu239') is None
+
     filename = str(tmpdir.join('test.xml'))
     lib.export_to_xml(filename)
     assert os.path.exists(filename)
@@ -29,9 +32,9 @@ def test_data_library(tmpdir):
     new_lib = openmc.data.DataLibrary()
     directory = os.path.dirname(os.environ['OPENMC_CROSS_SECTIONS'])
     new_lib.register_file(os.path.join(directory, 'H1.h5'))
-    assert new_lib.libraries[-1]['type'] == 'neutron'
+    assert new_lib[-1]['type'] == 'neutron'
     new_lib.register_file(os.path.join(directory, 'c_Zr_in_ZrH.h5'))
-    assert new_lib.libraries[-1]['type'] == 'thermal'
+    assert new_lib[-1]['type'] == 'thermal'
 
 
 def test_depletion_chain_data_library(run_in_tmpdir):

tests/unit_tests/test_deplete_resultslist.py

@@ -74,7 +74,7 @@ def test_get_keff(res):
 def test_get_steps(unit):
     # Make a Results full of near-empty Result instances
     # Just fill out a time schedule
-    results = openmc.deplete.Results()
+    results = openmc.deplete.Results(filename=None)
     # Time in units of unit
     times = np.linspace(0, 100, num=5)
     if unit == "a":